Well the containment cells may be tossed aside for now but there could still be repercussions if the Rogues start blabbing about them to the media and the cops.
Also while there was indeed a violation of ethics, the only other option was to kill the metahumans and only Wells would have supported that given he is the Reverse Flash.
So they had the options of
1. illegal incarceration in the only place that COULD hold them
2. kill them
3. turn them loose again.
A possible 4th option would have been suspended animation, but that tech doesn't seem to exist, unless Wells suddenly developed it but that would likely have tipped his hand about being from the future as such tech would be rather advanced.
They could have kept them drugged with sedatives but that would be unreliable and dangerous.
They could have helped the proper authorities build containment units in an actual prison and seen that the metas got a proper chance of due process.